Schema for lsSnpPdb

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Schema for lsSnpPdb

Database: hg19 Primary Table: lsSnpPdb Row Count: 115,267 Data last updated: 2010-12-03
Format description: Mapping of SNPs to protein structures obtained from LS-SNP PDB
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`protId`	O60701	`varchar(255)`	values	Protein Id
`pdbId`	2q3e	`varchar(255)`	values	PDB id
`structType`	XRay	`enum('XRay', 'NMR')`	values	type of structure
`chain`	A	`char(1)`	values	PDB chain id
`snpId`	rs10010387	`varchar(255)`	values	dbSNP id
`snpPdbLoc`	363	`int(11)`	range	location of SNP in PDB chain (1-based AA index)

Connected Tables and Joining Fields


	uniProt.extDbRef.extAcc1 (via lsSnpPdb.pdbId) uniProt.extDbRef.acc (via lsSnpPdb.protId)

Sample Rows

protId	pdbId	structType	chain	snpId	snpPdbLoc
O60701	2q3e	XRay	A	rs10010387	363
O60701	2qg4	XRay	A	rs10010387	363
O60701	3itk	XRay	A	rs10010387	363
O60701	3khu	XRay	A	rs10010387	363
Q86UW6	2vkc	NMR	A	rs78903360	1668
P61769	3bhb	XRay	B	rs11553032	12
P61769	3bhb	XRay	B	rs11553035	14
P61769	3bhb	XRay	B	rs11553038	22
P61769	3bhb	XRay	B	rs11553042	36
P61769	3bhb	XRay	B	rs11553049	41

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.